Approximately 20 major malformations have been identified from the malformations registry data base for future investigations. Cases with the major birth defects of interest have been selected from the Congenital Malformations Registry along with suitable control subjects. Data from the Registry have been linked with the State's newborn screening program to identify filter paper samples for the first group of subjects. Samples have been selected and DNA has been extracted for the first projects. Single nucleotide polymorphisms (SNPs) have been selected for several projects. SNP genotyping is now complete for the first two studies, omphalocele and Hirschprung's disease. Sequencing for the Hirschsprung's disease project is nearly complete. Several other projects are at various states of completion ranging from samples being identified for DNA extraction to awaiting SNP genotype results from the laboratory. Additional projects are in the design phase. We have recently demonstrated that DNA from these filter paper samples can be used for genome wide association studies (GWAS), with SNP call rates over 97%. Evaluation of the copy number variant results from the GWAS is in progress.